Supplementary Materials

Sci. Signal., 26 February 2013
DOI: 10.1126/scisignal.2003629
Supplementary Materials for:

Protein Complex–Based Analysis Framework for High-Throughput Data Sets

Arunachalam Vinayagam,* Yanhui Hu, Meghana Kulkarni, Charles Roesel, Richelle Sopko, Stephanie E. Mohr, Norbert Perrimon*

*To whom correspondence should be addressed. E-mail: vinu{at}genetics.med.harvard.edu (A.V.); perrimon{at}receptor.med.harvard.edu (N.P.)

This PDF file includes:

  • Fig. S1. Schematic representation of protein complex scoring.
  • Fig. S2. Snapshots of the COMPLEAT Web interface.
  • Fig. S3. Complex enrichment results of baseline and EGF stimulus.
  • Fig. S4. Baseline compared with EGF stimulus common complexes.
  • Fig. S5. Baseline compared with EGF stimulus dynamic complexes: opposing effects.
  • Fig. S6. Baseline compared with EGF stimulus: baseline-specific dynamic complexes.
  • Fig. S7. Baseline compared with EGF stimulus: stimulus-specific dynamic complexes.
  • Fig. S8. Complex enrichment results of baseline and insulin stimulus.
  • Fig. S9. Baseline compared with insulin stimulus: common complexes.
  • Fig. S10. Baseline compared with insulin stimulus: baseline-specific dynamic complexes.
  • Fig. S11. Baseline compared with insulin stimulus: stimulus-specific dynamic complexes.
  • Table S1. Compilation of literature protein complexes for humans, Drosophila, and yeast.
  • Table S2. PPI data sets used to construct integrated PPI networks for humans, Drosophila, and yeast.
  • Table S3. Predicted protein complexes for humans, Drosophila, and yeast.
  • Table S4. Redundancy in the protein complex resource.
  • Table S5. Overlap of the literature and predicted complexes at the protein level.
  • Table S6. Proteome covered by the protein complex resources.
  • Table S7. Comparison of protein complexes with GO and KEGG with respect to co-citation.
  • Table S8. Comparison of protein complexes with GO and KEGG with respect to protein colocalization.
  • Table S9. Comparison of protein complexes with GO and KEGG with respect to gene coexpression.
  • Table S10. Annotation of the protein complex resource.
  • Table S11. Gene or protein input identifiers supported by the COMPLEAT.
  • Table S20. Dynamic phosphosites changing in response to insulin treatment.

[Download PDF]

Technical Details

Format: Adobe Acrobat PDF

Size: 2.27 MB

Other Supplementary Material for this manuscript includes the following:

  • Table S12 (Microsoft Excel format). Enriched protein complexes at baseline (mtDER-S2R+ cell line).
  • Table S13 (Microsoft Excel format). Enriched protein complexes at EGF stimulus (mtDER-S2R+ cell line).
  • Table S14 (Microsoft Excel format). Enriched protein complexes at baseline (S2R+ cell line).
  • Table S15 (Microsoft Excel format). Enriched protein complexes at insulin stimulus (S2R+ cell line).
  • Table S16 (Microsoft Excel format). Consistent protein complexes with respect to baseline versus EGF stimulus.
  • Table S17 (Microsoft Excel format). Dynamic protein complexes with respect to baseline versus EGF stimulus.
  • Table S18 (Microsoft Excel format). Consistent protein complexes with respect to baseline versus insulin stimulus.
  • Table S19 (Microsoft Excel format). Dynamic protein complexes with respect to baseline versus insulin stimulus.

[Download Tables S12-S19]

Technical Details

Format: Zip Archive

Size: 314 KB

 


Citation: A. Vinayagam, Y. Hu, M. Kulkarni, C. Roesel, R. Sopko, S. E. Mohr, N. Perrimon, Protein Complex–Based Analysis Framework for High-Throughput Data Sets. Sci. Signal. 6, rs5 (2013).

© 2013 American Association for the Advancement of Science

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882